I have looked in all the mime directories that I know of, including my ~/.kde directory and the KDE mime type configuration, and nowhere that I can tell is jar ever associated with application/zip.

Since xfce and Gnome are correct, it leads me to believe the configuration is in a KDE specific directory (like ~/.kde/share/mimelnk/), but I have not found anything. Even the magic files don't seem to be the problem as they use application/x-zip not application/zip.

Where could KDE possibly be pulling the zip association from?

I have tested this on konqueror, krusader & dolphin, all show the application/zip as the mime type (which by the way has only *.zip and *.ZIP listed as glob patterns).

Thanks for the follow up. That is actually a response from the bug I ended up filing for this problem against Ubuntu. It took a long time for it to be confirmed and then moved upstream. The ironic thing is that I stopped using KDE applications altogether due to problems running KDE4 apps in Gnome in Ubuntu Jaunty (painting issues mostly) so any fix won't matter much to me, but at least other java users that like KDE should be helped by it.